Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Sodium- and chloride-dependent GABA transporter 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g9869 g9869.t5 TSS g9869.t5 5770746 5770746
chr_1 g9869 g9869.t5 isoform g9869.t5 5771012 5776427
chr_1 g9869 g9869.t5 exon g9869.t5.exon1 5771012 5771169
chr_1 g9869 g9869.t5 exon g9869.t5.exon2 5771769 5771970
chr_1 g9869 g9869.t5 exon g9869.t5.exon3 5774693 5774836
chr_1 g9869 g9869.t5 exon g9869.t5.exon4 5774898 5775120
chr_1 g9869 g9869.t5 exon g9869.t5.exon5 5775173 5775517
chr_1 g9869 g9869.t5 exon g9869.t5.exon6 5775591 5776427
chr_1 g9869 g9869.t5 cds g9869.t5.CDS1 5775702 5776427
chr_1 g9869 g9869.t5 TTS g9869.t5 5776568 5776568

Sequences

>g9869.t5 Gene=g9869 Length=1909
ATGGATGTGAAATCTTTTGATGTGCCAAATATTAGTGGCATAGAAAAATCCTCGAATAAT
GGAAGCAATGTTGAAATTTCAACGTCATCTACTGTCAATTTAATTGAAGATCGAACAAAT
TGGAGTCGACCAATTGAATTTATTTTATCGTGCTTGAGGTAAATAAACTTGAATAAATAT
TGGTAAAAGTTTATAATTAATCTTGTTTTGAAAGGAATGGCGGTGGAGCTTTTTTACTGC
CATATTTTCTTGCAGCAGTTTTTATTGGTTTGCCAATATTTTTTGCTGAACTGATTACAG
GACAATATAGTGGACTTGGGCCGATTAAAGCTTATAGTTATCTTGCTCCGCTCTTTAAAG
GCTTGGGCTACTGCACATTTATGGTAATTTCTTTCGTCAGCATTTACTATCAACTGATTA
TTGCGTGGGTCTTATTTTATCTTTATTCGTCATTCTTTCCATCTCTTCGTTGGGGCACAT
GTGACAATGATTGGAATTCTGAAAACTGTTTCAGTACAATTGAAGATTTATATTGTCGTC
AAGAAAATGTTGGTAGTGCAAGTGATCAAATTTTCTATCGTGGTGGATGCAGAGAGATTA
ACGAAATTTGTTCAATTCACGATTTGGTGGGCGTTAATGCTAGCAATTGTATGAATACAA
CAACAAATGAACTTGTTCCCATTAATGATGTCATCACAAGAAGCCTCTCATCTGAAGAGT
TTTTCTATGAACATGTTCTTGGTATTGGTGATGCGAGATGGGACAACTTTGGTTATCCTC
GATGGCAAATGGTCATTTTTCTATTTCTTGGTTGGACACTTACATATTTGTGTTTAATCA
AAGGCGTTCAGTCAATGGGAAAAGTCGTCTATTTTACTGCCACATTTCCTTATGTCATTT
TAACAGCTCTCTTAATTCGCTCATTAACATTAGAAGGTTCTTATGAAGGCATCATGTTTT
ATATTACTCCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCCAGCAGTC
AAATTTTCTACTCATTTGGCTTAGCTTGTGGCAGTCTTGTGGCTTTAGCTTCTTTAAAAA
TAATTGCCATTTTGATGCAGTATTTATATCAATCATAAATTTTGGCACTGCTATTTTCGG
TGGTTTTGTAGTTTTTGCGACTCTTGGATTTTTATCAAATTCAATGCAACAACCTATTGA
TAATGTCGTAACTGGTGGCCCTGGTTTAACATTTATTACATATCCTGAAGCTATCCTATT
GATGCCATTGCCAAACCTTTGGGCAATTTTGTTTTTCCTCATGATGCTCATTTTGGGTTT
AGGTTCTCAATTCCCTGGTGTTCAAATGATTTCAACTTCAATTGTTGATCATTGGCCACA
TTTGAGAAATAAGGAATGGAAAGTGACAGCTGGAGTATGCATGAGTTGTTTTGTTCTCGG
TTTACCAATGACTTGTCATGGTGGAATTTATCTTTTTACTCTTATGGAATGGCATACAGC
AAGTTGGGCAATTTTATTAATTGGTGCAGCTGAAATTGTCATCTTTTCATGGGTCTATGG
AATAAATAACACACTCGATATGATTAAAGAGATGGGAATGAAATTCGTAAAAGTTACGAG
ATATTTCTGGAAAGCAGTATGGGTTGTTATAACACCAATTGGATCAGTTGCAATTTTCAT
CTTTATTTTAACTGATTTGGGACCAAGTGAATTTCGTGATTATGTTTTTCCTCTTTGGGC
TGATATCTTAGGTTGGATGTTTGGACTTGCAACGCTTGTTCCTTTTATTGTTTTCGCTAT
TTATCAATTAATTGTTGTAAAAGATAAGAAAACACTACTCAAACCAACAGATCTTTGGGG
CCCACAAGAAATCGATGGACAAAGGATTGATAGAGCAGTATTAGCTTAA

>g9869.t5 Gene=g9869 Length=241
MQQPIDNVVTGGPGLTFITYPEAILLMPLPNLWAILFFLMMLILGLGSQFPGVQMISTSI
VDHWPHLRNKEWKVTAGVCMSCFVLGLPMTCHGGIYLFTLMEWHTASWAILLIGAAEIVI
FSWVYGINNTLDMIKEMGMKFVKVTRYFWKAVWVVITPIGSVAIFIFILTDLGPSEFRDY
VFPLWADILGWMFGLATLVPFIVFAIYQLIVVKDKKTLLKPTDLWGPQEIDGQRIDRAVL
A

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g9869.t5 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 2 228 1.1E-53
4 g9869.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 27 46 1.2E-14
3 g9869.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 107 127 1.2E-14
5 g9869.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 150 170 1.2E-14
1 g9869.t5 Pfam PF00209 Sodium:neurotransmitter symporter family 2 210 4.9E-48
17 g9869.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 31 -
23 g9869.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 53 -
15 g9869.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 54 73 -
20 g9869.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 99 -
18 g9869.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 100 104 -
22 g9869.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 105 126 -
14 g9869.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 146 -
21 g9869.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 147 168 -
16 g9869.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 169 187 -
19 g9869.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 188 210 -
13 g9869.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 211 241 -
12 g9869.t5 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 214 30.134
11 g9869.t5 SUPERFAMILY SSF161070 SNF-like 4 209 6.02E-44
8 g9869.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 46 -
10 g9869.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
6 g9869.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 127 -
9 g9869.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
7 g9869.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 189 211 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016021 integral component of membrane CC

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed